SMTL ID : 3hcn.1

Hg and protoporphyrin bound Human Ferrochelatase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.1: 6 residues within 4Å: Chain A: C.132, R.208, S.338, C.339, C.342, C.347 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.132, A:C.339, A:C.342, A:C.347 FES.8: 6 residues within 4Å: Chain B: C.132, R.208, S.338, C.339, C.342, C.347 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.132, B:C.339, B:C.342, B:C.347

4 x CHD: CHOLIC ACID(Non-covalent)

CHD.2: 10 residues within 4Å: Chain A: M.35, T.36, L.37, R.51, P.202, S.204, V.241, M.244 Ligands: CHD.3, HEM.6 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:M.35, A:L.37, A:P.202, A:P.202 Hydrogen bonds: A:T.36 Water bridges: A:M.244 Salt bridges: A:R.50, A:R.51 CHD.3: 3 residues within 4Å: Chain A: L.37, R.50 Ligands: CHD.2 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.37 CHD.9: 13 residues within 4Å: Chain B: M.35, T.36, L.37, R.50, R.51, P.202, S.204, V.241, G.242, M.244 Ligands: CHD.10, HEM.14, SO4.15 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:M.35, B:L.37, B:P.202, B:P.202, B:V.241, B:M.244 Salt bridges: B:R.50, B:R.51 CHD.10: 5 residues within 4Å: Chain B: L.37, L.43, F.46, R.50 Ligands: CHD.9 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.37, B:L.43, B:F.46 Hydrogen bonds: B:R.50

3 x IMD: IMIDAZOLE(Non-covalent)

IMD.4: 5 residues within 4Å: Chain A: H.199, S.200, Q.238, W.246 Ligands: HEM.6 1 PLIP interactions: 1 interactions with chain A pi-Stacking: A:H.199 IMD.12: 6 residues within 4Å: Chain B: H.199, S.200, Q.238, S.239, W.246 Ligands: HEM.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.200 pi-Stacking: B:H.199 IMD.13: 6 residues within 4Å: Chain B: M.12, L.28, L.34, Y.101, S.133 Ligands: HEM.14 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.31

1 x BCT: BICARBONATE ION(Non-functional Binders)

BCT.5: 7 residues within 4Å: Chain A: M.12, L.34, Y.101, Y.127, S.133, T.134 Ligands: HEM.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.127 Water bridges: A:D.31

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.6: 24 residues within 4Å: Chain A: M.12, L.25, L.28, F.29, L.34, R.51, I.55, Y.59, Y.127, S.133, T.134, H.199, L.201, P.202, V.205, Y.212, W.246, A.272, F.273, H.277, I.278 Ligands: CHD.2, IMD.4, BCT.5 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:L.25, A:L.28, A:L.28, A:F.29, A:L.34, A:I.55, A:Y.127, A:T.134, A:H.199, A:V.205, A:Y.212, A:W.246, A:F.273, A:I.278 Hydrogen bonds: A:I.278 Salt bridges: A:R.51, A:H.199 pi-Stacking: A:H.199 HEM.14: 25 residues within 4Å: Chain B: M.12, L.25, L.28, F.29, L.34, R.51, I.55, Y.59, Y.127, S.133, T.134, H.199, L.201, P.202, V.205, Y.212, V.241, W.246, A.272, F.273, H.277, I.278 Ligands: CHD.9, IMD.12, IMD.13 18 PLIP interactions: 18 interactions with chain B, Hydrophobic interactions: B:L.25, B:L.28, B:L.28, B:F.29, B:L.34, B:I.55, B:Y.127, B:T.134, B:H.199, B:V.205, B:Y.212, B:W.246, B:F.273, B:I.278 Hydrogen bonds: B:I.278 Salt bridges: B:R.51, B:H.199, B:H.277

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 4 residues within 4Å: Chain A: R.51, K.54, K.240, V.241 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.241 Salt bridges: A:R.51, A:K.54 SO4.15: 5 residues within 4Å: Chain B: R.51, K.54, V.241, G.242 Ligands: CHD.9 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.242 Salt bridges: B:R.51, B:K.54

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 10 residues within 4Å: Chain A: P.213, Q.214, S.217, W.237, L.247 Chain B: P.213, Q.214, S.217, W.237, L.247 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.217, A:S.217 Water bridges: B:Q.214, B:W.237, B:G.248, A:W.237, A:W.237

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Medlock, A.E. et al., Product release rather than chelation determines metal specificity for ferrochelatase. J.Mol.Biol. (2009)

Release Date

2009-11-10

Peptides

Ferrochelatase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ferrochelatase, mitochondrial

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